CHAPTER 9: TAXONOMY

Taxonomy: science of classifying organisms. Two main purposes: to identify organisms + represent relationships among them. Most taxonomists hierarchical system of classification organisms are arranged in a graded series, ranked. Systems some ways artificial, arbitrary, limited. Greek philosopher Aristotle (384-322 B.C.) all creatures arranged in hierarchy of complexity. (sponges, simple organisms lowest humans highest). Ladder of nature, scala naturae: dominance of humans over all living things.

9.1 Taxonomic Systems

Swedish botanist Carl Linnaeus (1707-1778) developed present biological system of classification. His system based on organisms physical and structural features, operated on idea: more features organisms have in common = closer their relationship. Binomial nomenclature: assigns each organism a two-part scientific name using Latin words common language for all scientists. Scientific Name often characteristic, e.g. Castor Canadensis (Beaver: from Canada) First part of name: genus (plural, genera) first letter capitalized, can write alone. E.g. Acer (maple trees). Second part: species (group of organisms look alike, can interbreed under natural conditions fertile offspring.) never used alone. E.g. Acer Rubrum (Red Maple). Advantage of two-name system: indicates similarities in anatomy, embryology, evolutionary ancestry. E.g. NA black bear (Ursus Americanus), grizzly bear (Ursus Horribilis) closely related. Same genus.

Levels of Classification Taxa (sin*.[gular, taxon: categories used to classify organisms) = seven main levels Levels of Classification Dandelion Housefly Human Kingdom Plantae Animalia Animalia Phylum Tracheophyta Arthropoda Chordata Class Angiospermae Insecta Mammalia Order Aesterates Diptera Primates Family Compositae Muscidae Hominidae Genus Taraxacum Musca Homo Species Officinale Domestica Sapiens Originally first level = two kingdoms: plants and animals. Later, discovered single celled organisms have both plant and animal traits. Third kingdom Protista (kingdom originally proposed for all unicellular organisms such as the amoeba. Multicellular algae have been added). After Bacteria + cyanobacteria lack true nucleus (referred to as prokaryotes) = 4th kingdom, Monera. All other organisms eukaryotes. Later mushrooms and moulds are different from plants Fungi. 1969 Robert Whittaker five classification system: animalia, plantae, fungi, protesta, monera 1970s microbiologist Carl Woese studies archaebacteria (prokaryotic microorganisms) sufficiently distinct from bacteria constitute own kingdom. They thrive in harsh habitats possess cell walls (not containing peptidoglycan) + ribosome components, very different from those in Eubacteria (possess rigid cell wall composed of peptidoglycan, 3d polymer containing carbohydrate and protein subunits, and reproduce with binary fission, six kingdom system). Therefore: Monera became: Archaebacteria and Eubacteria (true bacteria). Phylogeny history of evolution of organisms. Relationships shown in phylogenetic tree, starting from the most ancestral form - includes branchings that lead to all descendants.

1996 DNA sequencing studies Carol Bult + Carl Woese some genes in archaebacteria related to genes of humans and other eukaryotes, unlike eubacteria archaebacteria should not contain the term bacteria. Suggested Archaea. Many microbiologists traditional kingdom systems should be replaced with system that reflects evolutionary history of life three-domain classification system. Evolutionary history + classification schemes are continually updated as more DNA evidence is collected and analyzed. Scientists regularly use classification manuals to conduct identification work use of dichotomous key two part key series of choices must be made, each leads to a new branch of the key. Result name of organism being identified.

The Key 1. a) baleen plates b) teeth 2. a) dorsal fin b) no dorsal fin 3. a) long pectoral fin. b) short pectoral fin. 4. a) no dorsal fin b) large dorsal fin 5. a) small nose b) large projection from nose 6. a) mouth on ventral b) mouth at the front of head

Go to 2. Go to 4. Go to 3. Bowhead Whale. Humpback whale Blue whale Go to 5. Killer Whale Go to 6 Narwhal Sperm Whale Beluga

Levels of Classification Kingdom Phylum Class Order Family Genus Species

Dandelion Plantae Tracheophyta Angiospermae Asterates Compositae Taraxacum Officinale

Housefly Animalia Anthropoda Insecta Diptera Muscidae Musca Domestica

Human Animalia Chordata Mammalia Primates Hominidae Homo Sapiens

9.2 Viruses
Classification systems examining existing living organisms, comparing modern with extinct Viruses (Latin = poison) not in six-kingdom system lifeless chemical, carries out no life function reproduces when invading cells => doesnt display most characteristics of living cells. -9 1934 early electron microscope used to view tiny virus particles Size: 20 to 400 nm (10 m) in D Virus inner nucleic acid core, surrounded by outer protective protein coat called capsid accounts for 95% of the total virus, gives the virus its particular shape. E.g. bacteriophages (phages): category of viruses: eaters of bacteria: unique tadpole shape, distinct head, tail region Sometimes lipid membrane encloses the capsid, e.g. HIV. Lipid layer may come from host cells membrane when the virus leaves the host. Viruses contain either DNA or RNA single or double strand

Viral Diversity/ Specificity Not every virus disease-causing agent/pathogen. E.g. tobacco mosaic virus: infects leaves of tobacco plant, do not appear to destroy plant tissue on large scale. First viruses to be described: disease agents of higher plants and animals. 1915 certain viruses can infect bacteria. 1940+ bacteriophages served main experimental objects for examining biological properties. Viruses are selective specific viruses enter only specific host cells. E.g. bacteriophages: restricted host range (limited # host species, tissues, cells that a virus can infect). Human cold (cells of human upper respiratory tract), AIDS (immune system). Contrast most plant viruses infect large variety of plants, swine flu. Viral Replication: process genetic material is duplicated before cell divides. And Entrance: virus chemically recognizes host cell, attaches. Whole virus/ DNA / RNA enters. Of protein + nucleic acid units. Molecular info in viral DNA/RNA directs host cell to replicate viral components (nucleic acids, enzymes, capsid proteins, etc) Of units: viral nucleic acids + enzymes + proteins brought together, assembled -> new virus particles. Of new virus particles: newly formed virus particles released from infected cell, host cell dies

Attachment Synthesis Assembly Release -

Process: Lytic Cycle: 25 to 45 minutes, can produce 300 new virus particles. Bacteriophage that causes lysis (destruction or bursting open) of host cell virulent phage. temperate phage viruses that have a lysogenic cycle virus coexists with cell, carried through generations without harm injects nucleic acid into host bacterium, doesnt control of cell nucleic acid is integrated into bacteriums DNA, acts as another set of genes. It is replicated along with host DNA, passed to daughter cells. Virus appears to be in dormant state: lysogeny Can be activated by stimulus: damage to DNA, separation of its nucleic acid from host chromosome, or temperature, etc. This triggers lytic cycle, virus becomes virulent.

Viruses and Human Health Many diseases virus attacks cells while reproducing => cause symptoms of disease. Most viral infections not destroyed by the sulfa drugs or antibiotics used against bacterial diseases. Some viruses remain dormant years before symptoms Cancer-causing viruses, oncogenic viruses, cause disease by adding specific genes to an infected cell turning it into a cancer cell. Vaccines can be used to prevent body reacts to vaccine like a real virus, produces antibodies. These stay, and the body is immune. Phylogeny Three theories: 1. At one time cellular organisms, lived as parasites. They depended less and less on their cellular components and evolved to their present form. 2. Viral ancestors free living, precellular forms, later became parasites of cellular organisms. 3. Viruses arose from detached fragments of genetic material of cellular organisms. Frontiers of Technology: Viral Vectors and Gene Therapy Gene therapy viruses (vectors, carriers) carry specially altered DNA cells 980s scientists transferred genes into mammalian cells viral vectors genetically altered mouse viruses. To create viral vector remove genes in virus, replace them with gene to be transferred, mixed with growing cells in laboratory. enters cell, deposits new gene in chromosome remains in cell, passed to daughter cells. Very low risk of causing problems. Sept 14, 1990 attempt to correct genetic disease (adenosine deeaminase ADA) deficiency in 4 year old ability to make antibodies. ADA inheriting 1 defective ADA gene from each parent little immunity, do not produce antibodies after vaccination. Low chances of recovery from disease. Gene therapy almost 10 years to develop. One step isolating normal ADA gene from human T-cell lymphocytes (white blood cells that fight off infections/cancer). Next step development of efficient method to transfer normal gene into human immune

9.3 Kingdoms Eubacteria (Bacteria) and Archaebacteria

Bacteria constitute most of the decomposers of dead plants + animals essential for converting + recycling natures raw materials into nutrients for living plants + animals. Archaebacteria Eubacteria Archae: early, primitive Heterotrophic or autotrophic Heterotrophic Reproduce asexually (binary fission) No peptidoglycan Live everywhere Thrive in harsh environments (swamps, high Cell wall w/ peptidoglycan salt concentration habitats, high temperatures, Most are helpful (vitamins, yogurts, probiotics) acidity mostly without oxygen (anaerobic Some arent (strep throat) conditions) conditions of early Earth. Most bacteria / cyanobacteria 3 groups: Methanogens (methane-producing), Extreme Thermophiles (110 degrees +), Extreme Halophiles (very salty water). Common Characteristics of Archaebacteria and Eubacteria Prokaryotic, single celled Contain no membrane-bound organelles (like nuclei or mitochondria) Single chromosome Reproduce asexually by binary fission

1. 2. 3. 4.

Identification and Classification of Eubacteria (most bacteria and cyano bacteria) Appearance: shapes: Spherical (coccus, cocci), Rod-Shaped (bacillus, bacilli), Spiral (Spirillum, spirilla) After division cocci and bacilli, sometimes spirilla pairs, cluster colonies (Myxobacteria), chains (Streptococcus Mutans) (filaments) of cells, clumps (Staphylococcus Aureus)

Respiration and Modes of Nutrition Respiration Obligate Aerobes (must have oxygen to survive: e.g. those that cause tuberculosis) Obligate Anaerobes (live in absence of oxygen: deep soils, marine, freshwater sediments obtain energy by fermentation => carbon dioxide and alcohol produce wide array of organic compounds: acetic acid) Facultative Anaerobes (prefer oxygen, but can live without)

Modes of Nutrition Heterotrophs obtain nutrients from other organisms Parasites obtain without contributing to health of host

Saphrophytes obtain from dead and decomposing organic matter treatment of sewage Autotrophs making food from inorganic substances by photosynthesis (carbon dioxide + water + energy = carbohydrates) or chemisynthesis (chemical reactions as energy source = carbohydrates)

Reproduction and Growth Binary Fission single strand of DNA replicates bacterium produces cell wall divides into 2 cells separate or remain attached, every 20 minutes Conjugation two conjugal bacteria (donor + recipient) cell to cell contact cytoplasmic bridge Plasmids (pieces of DNA): donor -> recipient recombination of DNA (altered set of characteristics) two bacteria separate Endospores- dormant or resting cells - bacteria (bacillus) adapt to survival during unfavourable environmental conditions. Formed inside bacterial cell, thickened wall - around genetic material +

cytoplasm remainder of original cell disintegrates resistant to heat, not easily destroyed. Suitable growing conditions wall breaks down, active bacterium emerges. Beneficial Effects of Bacteria Bacteria constitute most of decomposers of dead plants and animals essential for converting and recycling natures raw materials into nutrients

Frontiers of Technology: Poison-Eating Microorganisms Penta-chlorophenol (toxic wood preservative) seep from storage containers, contaminating nearby soil + underground water. Cost excavation and incineration (200 and 300 dollars per cubic metre) sometimes hundreds of tones of soil. Bacterium from genus Flavobacterium economical and efficient alternative Bacteria dismantle complex toxic penta molecules, leaving nontoxic carbon dioxide, water, harmless chlorides requiring only oxygen and nutrients in soil. Advantage: cost, once the toxic chemical has been removed, bacterium dies Gene-splicing techniques can greatly enhance ability of bacteria to destroy pollutants combining genes from different organisms e.g. super poison eating bacteria. Harmful Effects of Bacteria Causing disease: Bacillus anthracis first bacterium proven to cause a disease 1976 Legionnaires disease outbreak in Philadephia Legionella pneumophilia. Etc: tuberculosis, diphtheria, typhoid fever, bubonic plague (Black Death) How? numbers place tremendous material burden on hosts tissues that interfere with normal function / actually destroy cells and tissues / produce toxins Infectious diseases spread moisture droplets in the air, dust, direct contact, fecal contaminations, animal bites, wounds Methods of protection: sterilization, disinfection, use of antiseptics, extermination of disease animals, immunization, administration of antibiotics. Bacterial Resistance to Antibiotics age of antibiotics mid 1940s 2500+ natural antibiotics (chemicals produced synthetically or by microorganisms that inhibit growth or destroy certain other microorganisms) used to treat infections. Developed resistance variations within bacterial population. weak killed, strong reproduce, passing slightly varied genetic material Most common type of bacterial resistance bacteria -> R (resistance) factors plasmids, special genes that code for enzymes that inactivate drugs transferred and recombined in conjugation. Did they exist before? conclusion: were widespread, but genes encoding for antibiotic resistance uncommon resistant strains become the dominant or common type.

9.4 Kingdom Protista

Eukaryotic cells recorded 1.5 billion years ago, more recent than bacteria differences: discrete, membrane-bound nucleus / contain organelles = more efficient method using nutrients + metabolic activities / includes simplest multicellular organisms (no true tissues) Once considered first animals placed in phylum: Protozoa. Recently, argued eukaryotic cells (animal-like or not) should be placed in separate kingdom: Protista. Plantlike Protists Contain chlorophyll (pigment that traps sunlight energy for photosynthesis) Used to be called algae: any photosynthetic organism, either unicellular or multicellular without tissues modern classification schemes: two kingdoms: Eubacteria (cyanbacteria, a.k.a. blue-green algae), Protista (red, brown, green algae). Example: Euglenophyta Phylum: Euglenids Description Has several features unique to protists, 800+ species in ponds and lakes Nutrition Mostly photosynthesis. Periods of darkness heterotrophic, take in solid food Stored in form of starch granules (like plants) Characteristics Eyespot - part of organisms sensory-motor system used to detect light Flagellum - propels organism through aquatic environments in whip-like fashion, most species have two Pellicle - entire outer boundary beneath plasma membrane surrounded firm, flexible covering (no cell wall) Central Nucleus, large green chloroplasts (identical to those in green algae + land plants, used to collect + remove excess water), vacuoles Reproduction Reproduces asexually following nuclear division, rest of the cell divides lengthwise longitudinal fission involves grown in cell circumference while organelles are being duplicated. Protection Unfavourable conditions thickly coated resting cell Green, Brown, Red Algae Chlorophyta, Phaeophyta, Rhodophyta - mostly multicellular, without tissues distinguishes them Algae: adapted to wet/moist environments. Normally aquatic organisms can be found in soils, lower trunks of trees, rocks. Brown + red algae (seaweeds) generally large multicellular oceanic plants. Unicellular green algae (phytoplankton) marine + freshwater, floating on + near water surface Brown + red algae: contain chlorophyll, other coloured pigments photosynthesis- with particular wavelengths of light Algae (esp. green algae) primary food producers in aquatic food chains / 67% of global oxygen human wastes + industrial contaminants may be reducing populations. Excess growth also problematic Food (source of vitamins, trace minerals), fertilizers Agar mucilaginous material, cell walls of red algae drug capsules, gels, cosmetics Carrageenan (similar) cosmetics, paints, ice cream, pie creating petroleum resources (brown algae) store food as oils after, die and sink to bottom of ocean, buried Millions of years, extreme heat, pressure transformed into crude oil deposits. variations among three phyla Chlorophyta, Phaeophyta, Rhodophyta range from complex life cycles, including both sexual + asexual reproduction simple asexual reproduction by fragmentation (organisms body breaks apart). Usually asexual by binary fission. Sometimes conjugation (Spirogyra)

Description Habitat

Nutrition Use

Reproduction

Animal-Like Protists (Protozoa) Heterotrophs must move most holozoic (engulf their food: bacteria and others) others saprozoic (absorb predigested or soluble nutrients directly through cell membranes) Classification: type of locomotion: life cycle: mode of reproduction: nutrition: free-living or parasitic important in modern identification + classification at lower taxonomic levels Protozoans rival bacteria population numbers, number of species occupy diverse range of moist habitats, range in size is considerable (2 micrometers (small mammalian red blood cell may contain dozens) 5cm in diameter e.g. foraminiferans).

Reproduction: usually asexual, binary fission. Adverse conditions protozoans form resting cells cysts (hardened protective covering on top of cell membrane) later emerging. Phylum Sarcodina Most free-living forms (except for few parasitic species in animal intestines) pseudopods (fingerlike projections for locomotion and food capture) divided into four groups: amoeba, foraminiferans, radiolarians, heliozoans. E.g.: Amoeba largest, least complex no shells moves by repeatedly extending, retracting its pseudopods. Cytoplasm has two layers: ectoplasm (thin semirigid, gelled layer under plasma membrane), endoplasm (more fluid part that fills inside of cell, responsible for ameobas shape as it moves) Linnaeus named - chaos chaos Feeds by phagocytosis pseudopods flow around + engulf food particles enclosed in food vacuole, where food is digested. Water taken in, along with extra water (diffusion) collects in contractile vacuole once full, contracts and water is discharged through pore in plasma membrane. binary fission amoeba splits, two organisms grow to full size, split again

Description Classification

Nutrition

Reproduction

Phylum Mastigophora Description Examples Animal-like flagellates one or more flagella live mainly in freshwater + marine habitats parasitic types other organisms Internal parasite e.g. Giardia lamblia causes stomach upsets + diarrhea, some severe effects. Often in cattle and wild animals, passes to humans when they drink water + eat food tained by feces of infected animals. Trichomonas vaginalis passed through sexual intercourse, result in infection in urinary and reproductive tracts.

Phylum Ciliophora Locomotion Ciliates hairlike structures called cilia, sometimes covering entire surface shorter and more abundant than flagella. Free-moving organisms, cilia are synchronized for swimming. Vorticella, Stentor cilia attaches microorganism to the surface. Most advanced both freshwater + marine. Two nuclei: large one: macronucleus involved in reproduction (usually asexual by binary fission, periodically conjugation (pair join to combine genetic material. Following, daughter cells undergo fission) hundreds of poison-laden barbs discharged either to drive away predators / capture prey : trichocysts Paramecium oral groove, contains mouth leading to cavity called gullet specialized cilia sweeps away bacteria + other food particles into cavity. From gullet, food enters food vacuole (digestion). Wastes expelled from food vacuole through anal pore. Also collects water in contractile vacuole

Reproduction

Defense mechanism Examples

Phylum Sporozoa Locomotion Lack any means of independent locomotion (some have flagella while maturing) exclusively parasitic depend on body fluids of host for movement fewer organelles, specialized structures than others Complex life cycle have reproductive cells that can produce new organism without fertilization (pores) during life cycle sporozoites sometimes 2+ hosts involved parasite reproduces sexually in one host, asexually in the other. Insects usually responsible for transmitting from one host to next: insect vectors. Plasmodium malaria

Reproduction

Examples

Fungilike Protists slime moulds phylum Gymnomycota prefer cool, shady, moist places, usually found under fallen leaves, rotting logs. Name derived slimy trail left behind as mould moves over ground Some stage in life cycle resemble protozoans, become amoebalike or have flagella. Other times produce spores like single-celled organisms. E.g. Dictyostelium most of life cycle as single celled amoebalike organism they can converge into a large slimy mass plasmodium begins to act as single organism, extending sluglike form, beginning to creep, feeding organic matter is it goes slow .,